|
Status |
Public on Jun 01, 2010 |
Title |
Delta dksA Cells Replicate 2 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Delta dksA Cells
|
Organism |
Escherichia coli str. K-12 substr. MG1655 |
Characteristics |
growth stage: log phase strain: MG1655 delta lac delta dksA treatment: No treatment
|
Treatment protocol |
At OD600~0.3, serine hydroxamate was added to a final concentration of 0.5mg/ml, cells were collected 40 minutes later.
|
Growth protocol |
Cells were grown in M9 medium supplemented with 0.2% glucose and 0.4% casamino acid at 37℃
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions.
|
Label |
Cy5
|
Label protocol |
15 µg of RNA were primed with 2.5 µg of random hexamer at 70°C for 10 min, and reversed transcribed at 50°C for 1 h in the presence of 300 U SuperScript III RTase (Invitrogen), 5xRT Buffer, 10mM DTT, 20U RNaseOut (Invitrogen) and 500 µM each dATP, dCTP, dGTP, with 200 µM dTTP, 600 µM aa-dUTP. cDNA samples were incubated with Cy3 (reference) or Cy5 (sample) for 2hrs.
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|
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Channel 2 |
Source name |
pooled reference RNA
|
Organism |
Escherichia coli str. K-12 substr. MG1655 |
Characteristics |
growth stage: log phase strain: MG1655 delta lac + MG1655 delta lac delta dksA treatment: Pooled RNA from mixture of the same amount of wt, wt+SHX, dksA, dksA+SHX RNA samples
|
Treatment protocol |
At OD600~0.3, serine hydroxamate was added to a final concentration of 0.5mg/ml, cells were collected 40 minutes later.
|
Growth protocol |
Cells were grown in M9 medium supplemented with 0.2% glucose and 0.4% casamino acid at 37℃
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using QIAGEN RNeasy Mini Kit following manufacturer's instructions.
|
Label |
Cy3
|
Label protocol |
15 µg of RNA were primed with 2.5 µg of random hexamer at 70°C for 10 min, and reversed transcribed at 50°C for 1 h in the presence of 300 U SuperScript III RTase (Invitrogen), 5xRT Buffer, 10mM DTT, 20U RNaseOut (Invitrogen) and 500 µM each dATP, dCTP, dGTP, with 200 µM dTTP, 600 µM aa-dUTP. cDNA samples were incubated with Cy3 (reference) or Cy5 (sample) for 2hrs.
|
|
|
|
Hybridization protocol |
Hybridization was performed following Agilent Two-Color Microarray-Based Prokaryote Analysis Protocol.
|
Scan protocol |
Scanned on a GenePix 4000B Scanner (Axon Instruments).
|
Description |
Biological replicate 2 of 3. MG1655 delta lac delta dksA cells untreated
|
Data processing |
GenePix Pro (v 6.1) was used for background subtraction and normalization.
|
|
|
Submission date |
Jan 05, 2010 |
Last update date |
Jan 05, 2010 |
Contact name |
Jue D. Wang |
Organization name |
Baylor College of Medicine
|
Department |
Molecular and Human Genetics
|
Lab |
Wang
|
Street address |
1 Baylor Plaza, Rm T932
|
City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
|
|
Platform ID |
GPL9855 |
Series (1) |
GSE19742 |
Expression profiling of E.coli K-12 wild-type vs. delta dksA cells upon amino acid starvation |
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